Multi Site and MySQL replication

How are you replicating between the multisites?

I am using MySQL replication that replicates from instance one to instance two

Okay, in that replication, you’ll have to search/replace the old domain for the new one.

Most of us use this for that job, since it handles the data serialization: https://interconnectit.com/products/search-and-replace-for-wordpress-databases/

Right now I have a script that replaces the domain names, and have a cron job running every couple mins. There is a snippet of code on our portal that goes to the other instance everytime a new post is posted. So there are times where the snippet and my script is not in sync. That is causing the problems to users. Is there any other direct solution.

*points to the script above*

There’s no ‘direct’ solution becuase WP itself doesn’t lend itself to doing that. You need to edit your script so that it’s processing the SERIALIZED data. And since we can’t see your script, that’s all we can tell you.